{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Comparing Multinomial and Gaussian Naive Bayes\n",
    "\n",
    "scikit-learn documentation: [MultinomialNB](http://scikit-learn.org/stable/modules/generated/sklearn.naive_bayes.MultinomialNB.html) and [GaussianNB](http://scikit-learn.org/stable/modules/generated/sklearn.naive_bayes.GaussianNB.html)\n",
    "\n",
    "Dataset: [Pima Indians Diabetes](https://archive.ics.uci.edu/ml/datasets/Pima+Indians+Diabetes) from the UCI Machine Learning Repository"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# read the data\n",
    "import pandas as pd\n",
    "url = 'https://archive.ics.uci.edu/ml/machine-learning-databases/pima-indians-diabetes/pima-indians-diabetes.data'\n",
    "col_names = ['pregnant', 'glucose', 'bp', 'skin', 'insulin', 'bmi', 'pedigree', 'age', 'label']\n",
    "pima = pd.read_csv(url, header=None, names=col_names)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pregnant</th>\n",
       "      <th>glucose</th>\n",
       "      <th>bp</th>\n",
       "      <th>skin</th>\n",
       "      <th>insulin</th>\n",
       "      <th>bmi</th>\n",
       "      <th>pedigree</th>\n",
       "      <th>age</th>\n",
       "      <th>label</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>6</td>\n",
       "      <td>148</td>\n",
       "      <td>72</td>\n",
       "      <td>35</td>\n",
       "      <td>0</td>\n",
       "      <td>33.6</td>\n",
       "      <td>0.627</td>\n",
       "      <td>50</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>85</td>\n",
       "      <td>66</td>\n",
       "      <td>29</td>\n",
       "      <td>0</td>\n",
       "      <td>26.6</td>\n",
       "      <td>0.351</td>\n",
       "      <td>31</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>8</td>\n",
       "      <td>183</td>\n",
       "      <td>64</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>23.3</td>\n",
       "      <td>0.672</td>\n",
       "      <td>32</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1</td>\n",
       "      <td>89</td>\n",
       "      <td>66</td>\n",
       "      <td>23</td>\n",
       "      <td>94</td>\n",
       "      <td>28.1</td>\n",
       "      <td>0.167</td>\n",
       "      <td>21</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0</td>\n",
       "      <td>137</td>\n",
       "      <td>40</td>\n",
       "      <td>35</td>\n",
       "      <td>168</td>\n",
       "      <td>43.1</td>\n",
       "      <td>2.288</td>\n",
       "      <td>33</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   pregnant  glucose  bp  skin  insulin   bmi  pedigree  age  label\n",
       "0         6      148  72    35        0  33.6     0.627   50      1\n",
       "1         1       85  66    29        0  26.6     0.351   31      0\n",
       "2         8      183  64     0        0  23.3     0.672   32      1\n",
       "3         1       89  66    23       94  28.1     0.167   21      0\n",
       "4         0      137  40    35      168  43.1     2.288   33      1"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# notice that all features are continuous\n",
    "pima.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# create X and y\n",
    "X = pima.drop('label', axis=1)\n",
    "y = pima.label"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# split into training and testing sets\n",
    "from sklearn.cross_validation import train_test_split\n",
    "X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# import both Multinomial and Gaussian Naive Bayes\n",
    "from sklearn.naive_bayes import MultinomialNB, GaussianNB\n",
    "from sklearn import metrics"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.541666666667\n"
     ]
    }
   ],
   "source": [
    "# testing accuracy of Multinomial Naive Bayes\n",
    "mnb = MultinomialNB()\n",
    "mnb.fit(X_train, y_train)\n",
    "y_pred_class = mnb.predict(X_test)\n",
    "print metrics.accuracy_score(y_test, y_pred_class)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.791666666667\n"
     ]
    }
   ],
   "source": [
    "# testing accuracy of Gaussian Naive Bayes\n",
    "gnb = GaussianNB()\n",
    "gnb.fit(X_train, y_train)\n",
    "y_pred_class = gnb.predict(X_test)\n",
    "print metrics.accuracy_score(y_test, y_pred_class)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Conclusion:** When applying Naive Bayes classification to a dataset with **continuous features**, it is better to use Gaussian Naive Bayes than Multinomial Naive Bayes. The latter is suitable for datasets containing **discrete features** (e.g., word counts).\n",
    "\n",
    "Wikipedia has a short [description](https://en.wikipedia.org/wiki/Naive_Bayes_classifier#Gaussian_naive_Bayes) of Gaussian Naive Bayes, as well as an excellent [example](https://en.wikipedia.org/wiki/Naive_Bayes_classifier#Sex_classification) of its usage."
   ]
  }
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